1N6K: Ras-related protein Rab-5A

Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride. Determined by X-ray diffraction at 1.55 Å resolution. Released 27 Nov 2002.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,627
Mol. weight: 19.64 kDa
Ligands: MG, AF3, GDP
Released: 27 Nov 2002

Explore 1N6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N6K contains 8 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-26	10	1
α-helix	33-42	10
α-helix	49-52	4
β-strand	55-64	10	1
β-strand	67-76	10	1
α-helix	80-85	6
α-helix	86-90	5
β-strand	95-101	7	1
α-helix	105-121	17
β-strand	127-133	7	1
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-161	4	1
α-helix	170-179	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-5A	A	protein	170	Homo sapiens	P20339 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1N6K_1 Ras-related protein Rab-5A (chains A)
GNKICQFKLVLLGESPVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIW
DTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNK
ADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
AF3	Aluminum fluoride	Al F3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Water and common crystallization additives (BME) are not listed.

Primary citation

High Resolution Crystal Structures of Human Rab5a and Five Mutants with Substitutions in the Catalytically Important Phosphate-Binding Loop. Zhu, G., Liu, J., Terzyan, S. et al. J Biol Chem (2003) 278:2452-2460. DOI 10.1074/jbc.M211042200 · PubMed

Other PDB entries of the same protein (UniProt P20339 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1R2Q 1.05 Å, Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution
1N6H 1.51 Å, Crystal Structure of Human Rab5a
1N6P 1.54 Å, Crystal Structure of Human Rab5a A30E mutant complex with GppNHp
1N6R 1.55 Å, Crystal Structure of Human Rab5a A30L mutant complex with GppNHp
1N6I 1.6 Å, Crystal Structure of Human Rab5a A30P mutant Complex with GDP
1N6L 1.6 Å, Crystal Structure of Human Rab5a A30P mutant complex with GTP
1N6N 1.6 Å, Crystal Structure of Human Rab5a A30R mutant complex with GppNHp
1N6O 1.8 Å, Crystal Structure of Human Rab5a A30K mutant complex with GppNHp
3MJH 2.03 Å, Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1
1TU4 2.2 Å, Crystal Structure of Rab5-GDP Complex
1TU3 2.31 Å, Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain
9RX5 3.15 Å, VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)

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